Sequence
atgc intronic sequence ATGC exonic sequencegtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24620.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g29070.1 (Oryza sativa), 3'ss of exon 7
----gtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
| || || | | | | || | || | | ||| ||| || | | | || | | | | | | || |||||||||||||| ||||| ||||||||||| || | || || ||| | ||| |||| ||||| ||||||||||| || || || || ||||| ||||| |
gttagcattgttgattacttctgtttaagttttt----ttgtca------ttgttttgtgcattatttttatgttttgagttgaacatatgtttcagGATATGGTTGTACTTCCGTACAAGGATAGTTTGCTACTTTTGAGTAGATATTTGCAACAGCTTGTCATGGAATCTCTTGGGAAAGAATTTGACCTTGATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G076075_T01 (Zea mays), 3'ss of exon 6
gtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
|| | | ||| || ||| | | |||| | || || ||||||| | |||| | | | || ||||||| |||||||||||||| ||||||||||||||||| ||||| || || ||| | ||| |||| || || ||||||||||| || ||||| || || || || || |
gtttgcaacatcattgattgggagcatctt----ctattgatga-atgttgttcttactttcctttat----tgatttttttttcttt--cagGATATGGTTGTGCTTCCTTACAAGGATAGTTTATTACTTTTGAGTAGATATTTGCAACAACTTGTCATGGAATCTCTTGGAAAAGAATTCGACCTGGATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G140614_T02 (Zea mays), 3'ss of exon 7
gtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
||| | || | || || || | |||| | || || ||||||| | || | || |||| || | || |||||||||||||| ||||||||||||||||| || ||||| || ||| | ||| |||| || || ||||||||||| || || || || |||||||| || |
---gtttacagcatcattgtttgtagcatttt--ctattgatga-atgttgttcttacttactgttttg---tatttttatctcatt---cagGATATGGTTGTACTTCCTTACAAGGATAGTTTGTTGCTTTTGAGTAGATATTTGCAACAACTTGTCATGGAATCTCTTGGGAAAGAATTTGATCTGGATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G37590.1 (Glycine max), 3'ss of exon 7
gtgtttttcctcaact-----tttttgagagttctaaggcta-----tcaaggagattgagttcttattgaccttattactctattcttgctttct--tttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
|| | || | | | ||| ||| | | || || | || ||||| | | ||| || | |||| | | |||||||||||| ||||||| || ||||| ||||| || |||||||| | || |||| ||| ||||||||||||| ||||| ||||||||||| | | |
gtatggatcatagagtaatagtttatgaatgattagcaactgacttctcttctgtttcttgtcactattgcttattatgatcttctcctcctttttattcctcagGATATGGTTATCCTTCCATATAAGGACAGCTTGTTATTATTTAGTAGATACTTGCAACAGTTGGTCATGGAATCTCTAGGCAAGGAGTTTGACTTGAATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G09800.1 (Glycine max), 3'ss of exon 7
gtgtttttcctcaacttttttgagagttctaa--ggctatcaaggagattgagttcttattgac-----cttattactctattcttgctttc-ttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
||||| || | | || || | || ||| | ||||| || ||| | | || | | | || | ||||||||||| | ||||| |||||||| ||| | || |||| ||| | || |||||||||||||||||||||| ||||| ||||||||||| | || |
-------------------gtgagaattatgatcggttagcgtctgtcttctgttttatttgactatttctcattgttttcttttccttcttattctgtagGATATGGTTATTCTTCCATACAAGGACAGCCTGTTATTATTCAGTAGATACTTGCAGCAGCTGGTCATGGAATCTCTAGGCAAGGAGTTTGACTTGGATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G09880.1 (Glycine max), 3'ss of exon 7
gtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
| || ||| | | | || || || | |||| | | | ||| ||| | ||| || | ||||||||||| | ||||| |||||||| ||| | || |||| ||| | || |||||||||||||||||||||| ||||| ||||||||||| | || |
----------gtgagaattatgatcggttagcgtctgtcttatgttttatttgactatttctcatcgttttcttttccttctta-ttctgtagGATATGGTTATTCTTCCGTACAAGGACAGCCTGTTATTATTCAGTAGATACTTGCAGCAGCTGGTCATGGAATCTCTAGGCAAGGAGTTTGACTTGGATG
upper sequence: AT4G24620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g07280.t01 (Vitis vinifera), 3'ss of exon 7
------gtgtttttcctcaact--tttttga-gagttctaaggctatcaaggagattgagttcttattgaccttattactctat-tcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
| || ||| | | | || | | | | | | || | || | ||| | || || | | ||||| ||| | ||||||||||||| | |||||||||||||| |||||||| |||| ||| ||||| ||||||| ||||||||||||||| | |||||||||||||| || || |
gtcttaacctcttcactctattgatcattaatgcagtgtcttgttgtctcataatctgtttcactataaataactttgctttgtctcttggttt--tccacagGATATGGTTATTCTTCCTTACAAGGACAGCTTATTATTATTCAGTAGGTATTTGCAGCAACTGGTCATGGAATCAATTGGAAAGGAGTTTGACCTGGATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86063838|gb|DR359595.1|DR359595EST: CGCTCTTAGCTATGTGTTGGTACTGGGCTTCCAATGGCGTTGGTTCCAAG GATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTAT
genomic: CGCTCTTAGCTATGTGTTGGTACTGGGCTTCCAATGGCGTTGGTTCCAAGgtgtttttcc ... tcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
tattgac putative branch site (score: 2)
ccttattactctattc CT-rich tract
tttctttta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttttcctcaacttttttgagagttctaaggctatcaaggagattgagttcttattgaccttattactctattcttgctttcttttacagGATATGGTTGTCCTTCCTTACAAGGATAGCTTATTGCTATTTAGTCGGTATCTGCAGCAGCTGGTCATGGAATCACTAGGAAAGGAGTTTGATCTTGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG